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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4fliY16Methionine aminopeptidase 1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4fliY16Methionine aminopeptidase 1/1.000
4iktTFVMethionine aminopeptidase 1/0.738
4ikuSHXMethionine aminopeptidase 1/0.707
4ikrPVPMethionine aminopeptidase 1/0.684
4flkY10Methionine aminopeptidase 1/0.668
4fllYZ6Methionine aminopeptidase 1/0.668
4fljY08Methionine aminopeptidase 1/0.661
4hxx1AYMethionine aminopeptidase 1/0.652
3pkeY10Methionine aminopeptidase 2/0.647
3pkaY02Methionine aminopeptidase 2/0.646
3pkdY10Methionine aminopeptidase 2/0.646
1c23MPHMethionine aminopeptidase/0.633
3iu7FCDMethionine aminopeptidase 2/0.631
2evcFC3Methionine aminopeptidase/0.630
3pkbY16Methionine aminopeptidase 2/0.624
3iu8T03Methionine aminopeptidase 2/0.621
2q92B23Methionine aminopeptidase/0.619
2evmFC2Methionine aminopeptidase/0.617
3pkcY08Methionine aminopeptidase 2/0.602
2q93B21Methionine aminopeptidase/0.596
2nq7HM5Methionine aminopeptidase 1/0.585
2gg8U15Methionine aminopeptidase/0.584
2q94A04Methionine aminopeptidase/0.582
2q96A18Methionine aminopeptidase/0.582
2p99YE6Methionine aminopeptidase/0.574
4iksTFDMethionine aminopeptidase 1/0.574
2g6pHM2Methionine aminopeptidase 1/0.573
1r5gAO1Methionine aminopeptidase 2/0.572
2ggbU17Methionine aminopeptidase/0.568
2gg3U13Methionine aminopeptidase/0.559
3d27W29Methionine aminopeptidase/0.547
2gg0U11Methionine aminopeptidase/0.545
2p98YE7Methionine aminopeptidase/0.538
1xnzFCDMethionine aminopeptidase/0.531
2ga2A19Methionine aminopeptidase 2/0.523
2gg9U16Methionine aminopeptidase/0.519
2ea2F77Methionine aminopeptidase 2/0.517
1r5hAO2Methionine aminopeptidase 2/0.516
3iu9T07Methionine aminopeptidase 2/0.515
1r58AO5Methionine aminopeptidase 2/0.504
1yw8A75Methionine aminopeptidase 2/0.498
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.498
2ea4F79Methionine aminopeptidase 2/0.497
1q84TZ4Acetylcholinesterase3.1.1.70.496
1yw9A84Methionine aminopeptidase 2/0.496
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.494
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.493
1qzyTDEMethionine aminopeptidase 2/0.492
1gpnHUBAcetylcholinesterase3.1.1.70.491
1h60STRPentaerythritol tetranitrate reductase/0.482
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.481
2xugTZ4Acetylcholinesterase3.1.1.70.480
2oazI96Methionine aminopeptidase 2/0.479
4ey6GNTAcetylcholinesterase3.1.1.70.479
2jf0HBPAcetylcholinesterase3.1.1.70.477
2gg2U12Methionine aminopeptidase/0.476
2w6cBM4Acetylcholinesterase3.1.1.70.476
2xupTZ5Acetylcholinesterase3.1.1.70.475
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.475
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.474
2whqHI6Acetylcholinesterase3.1.1.70.471
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.471
4ey7E20Acetylcholinesterase3.1.1.70.471
2cekN8TAcetylcholinesterase3.1.1.70.469
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.469
1votHUPAcetylcholinesterase3.1.1.70.468
2ckmAA7Acetylcholinesterase3.1.1.70.468
4drn0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.468
3rvhHQ2Lysine-specific demethylase 4A1.14.110.467
3h0bB35Beta-secretase 13.4.23.460.466
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.466
3v0o4GWHisto-blood group ABO system transferase/0.466
2j3qTFLAcetylcholinesterase3.1.1.70.465
4m0f1YKAcetylcholinesterase3.1.1.70.465
1gaxVAAValine--tRNA ligase6.1.1.90.464
1h22E10Acetylcholinesterase3.1.1.70.464
1odcA8BAcetylcholinesterase3.1.1.70.464
2xukTZ5Acetylcholinesterase3.1.1.70.464
2xuoTZ4Acetylcholinesterase3.1.1.70.464
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.464
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.464
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.462
2rqfJH3Hemolymph juvenile hormone binding protein/0.462
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.461
2jl1NAPTriphenylmethane reductase/0.461
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.461
2wzySQXSoluble acetylcholine receptor/0.460
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.460
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.460
1e66HUXAcetylcholinesterase3.1.1.70.459
1vbiNADMalate/L-lactate dehydrogenase family protein/0.459
1w6rGNTAcetylcholinesterase3.1.1.70.459
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.459
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.458
4araC56Acetylcholinesterase3.1.1.70.458
1ex75GPGuanylate kinase2.7.4.80.457
1qtiGNTAcetylcholinesterase3.1.1.70.457
2xujTZ5Acetylcholinesterase3.1.1.70.457
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3h3qH13Collagen type IV alpha-3-binding protein/0.457
3pdqKC6Lysine-specific demethylase 4A1.14.110.457
3wqmB29Diterpene synthase3.1.7.80.457
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4yp6NAPNicotinamide-nucleotide adenylyltransferase2.7.7.10.456
3junAJDPhenazine biosynthesis protein A/B/0.455
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4j0v1H7Beta-secretase 13.4.23.460.455
1eveE20Acetylcholinesterase3.1.1.70.454
1yw7A41Methionine aminopeptidase 2/0.454
2zevIPEGeranylgeranyl pyrophosphate synthase/0.454
3e6eDCSAlanine racemase/0.454
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.454
3w3nRX8Toll-like receptor 8/0.454
1sdwIYTPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.453
4arbC57Acetylcholinesterase3.1.1.70.453
4gddNAIUDP-galactopyranose mutase/0.453
4lutDCSAlanine racemase/0.453
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.453
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.452
3t0iSAHPutative methyltransferase/0.452
4dh0MR8Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.452
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4zwpM44Xaa-Pro dipeptidase3.4.13.90.452
1dx6GNTAcetylcholinesterase3.1.1.70.451
1xddAAYIntegrin alpha-L/0.451
2pb1NFGGlucan 1,3-beta-glucosidase/0.451
2xi4AFTAcetylcholinesterase3.1.1.70.451
2xufTZ4Acetylcholinesterase3.1.1.70.451
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.451
3i0oSMISpectinomycin phosphotransferase/0.451
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4b7zQ4QAcetylcholinesterase3.1.1.70.450
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.450
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
4ts7ADPPurine phosphoribosyltransferase (GpT-1)/0.450
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.449
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.449
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3p62FMNPentaerythritol tetranitrate reductase/0.449
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1zgbA1EAcetylcholinesterase3.1.1.70.448
2ct8MSPMethionine--tRNA ligase6.1.1.100.448
3b1dPLSBetaC-S lyase/0.448
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.448
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.448
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.448
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.448
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.448
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.448
1kwcBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.447
2ha6SCKAcetylcholinesterase3.1.1.70.447
2hxzH7JCathepsin S3.4.22.270.447
2q3oFMN12-oxophytodienoate reductase 31.3.1.420.447
3akn11DFatty acid-binding protein, intestinal/0.447
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3juoAJDPhenazine biosynthesis protein A/B/0.447
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.447
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.446
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
1zgcA2EAcetylcholinesterase3.1.1.70.446
1zw9H64ATP-dependent molecular chaperone HSP82/0.446
2c20NADUDP-glucose 4-epimerase/0.446
2gyuHI6Acetylcholinesterase3.1.1.70.446
2vd7PD2Lysine-specific demethylase 4A1.14.110.446
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3ufl508Beta-secretase 13.4.23.460.446
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4h2w5GPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.446
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.446
1rp7TZDPyruvate dehydrogenase E1 component1.2.4.10.445
2gywOBIAcetylcholinesterase3.1.1.70.445
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.445
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.445
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.445
2xb9XNW3-dehydroquinate dehydratase4.2.1.100.445
3af1GDPPantothenate kinase2.7.1.330.445
3b4p3B4Phenazine biosynthesis protein A/B/0.445
3dz6M8ES-adenosylmethionine decarboxylase proenzyme4.1.1.500.445
3fktSIIBeta-secretase 13.4.23.460.445
3mjrAC2Deoxycytidine kinase2.7.1.740.445
4b66NAPL-ornithine N(5)-monooxygenase/0.445
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.445
1ndiCOACarnitine O-acetyltransferase2.3.1.70.444
3b6pTMPThree-prime repair exonuclease 13.1.11.20.444
3ccc7ACDipeptidyl peptidase 4/0.444
3fazNOSPurine nucleoside phosphorylase/0.444
3l5lFMNXenobiotic reductase/0.444
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.444
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.444
4gd40WSLysine-specific demethylase 4A1.14.110.444
4l0oPLPCystathionine gamma-synthase2.5.1.480.444
5d5aCAUBeta-2 adrenergic receptor/0.444
2dg4RAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.443
2oz57XYUncharacterized protein/0.443
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.443
2xuhTZ4Acetylcholinesterase3.1.1.70.443
3g0gRUMDipeptidyl peptidase 4/0.443
3n87N873-dehydroquinate dehydratase4.2.1.100.443
3o5rFK5Peptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.443
3pzcGAPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.443
4awsFMNNADH:flavin oxidoreductase Sye1/0.443
4azaMGOEukaryotic translation initiation factor 4E/0.443
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.443
4i101BSBeta-secretase 13.4.23.460.443
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.443
1ut6A8NAcetylcholinesterase3.1.1.70.442
2aotSAHHistamine N-methyltransferase2.1.1.80.442
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.442
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3g0bT22Dipeptidyl peptidase 4/0.442
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.442
3sxjSAMPutative methyltransferase/0.442
4m0cFMNFMN-dependent NADH-azoreductase 1/0.442
4psbGA3Cytokinin-specific binding protein/0.442
4xbjIN5Alanine racemase, biosynthetic/0.442
1qpf858Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.441
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
2a4xBLMMitomycin-binding protein/0.441
2aouCQAHistamine N-methyltransferase2.1.1.80.441
2e0nSAHPrecorrin-2 C20-methyltransferase/0.441
2xuiTZ5Acetylcholinesterase3.1.1.70.441
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3vilSA0Beta-glucosidase/0.441
4bfwZVWPantothenate kinase2.7.1.330.441
1a4wQWEProthrombin3.4.21.50.440
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.440
2aot2PMHistamine N-methyltransferase2.1.1.80.440
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2pucGUNHTH-type transcriptional repressor PurR/0.440
2rlcCHDCholoylglycine hydrolase3.5.1.240.440
3f8sPF2Dipeptidyl peptidase 4/0.440
3zv7NHGAcetylcholinesterase3.1.1.70.440
4b70WM9Beta-secretase 13.4.23.460.440
4bb2STRCorticosteroid-binding globulin/0.440
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4j0t6T9Beta-secretase 13.4.23.460.440
5a8aADPRiboflavin biosynthesis protein RibF2.7.1.260.440
5d6lCAUBeta-2 adrenergic receptor/0.440